It turns out that the flu virus is surprisingly bad at making flu virions

In order to successfully infect a cell an influenza virus needs a small collection of proteins that are absolutely essential, and it looks like at least 90% of all individual influenza virions is lacking at least one of them, weird huh? Influenza mutates extraordinarily fast in order to outrun the immune systems of its host populations, generating new patterns that its hosts’ immune systems haven’t seen before by the time they are exposed again next flu season, and it seems like this must be just a natural consequence of how it does that.  These results do call for a re-orientation in how we see influenza infection, in addition to potentially infection by many phages, as they show that not only must new hosts be infected by a population of distinct virions but indeed also each cell.

Influenza virusInfluenza Virus with its parts, Source: http://micro.magnet.fsu.edu/cells/viruses/influenzavirus.html

Most Influenza A Virions Fail to Express At Least One Essential Viral Protein (PDF)

CB Brooke, WL Ince, et al. Published 2013 in J. Virol. doi: 10.1128/​JVI.02284-12

Segmentation of the influenza A virus (IAV) genome enables rapid gene reassortment at the cost of complicating the task of assembling the full viral genome. By simultaneously probing for the expression of multiple viral proteins in MDCK cells infected at low multiplicity with IAV, we observe that the majority of infected cells lack detectable expression of one or more essential viral proteins. Consistent with this observation, up to ninety percent of IAV-infected-cells fail to release infectious progeny, indicating that many IAV virions scored as non-infectious by traditional infectivity assays are capable of single-round infection. This fraction was not significantly affected by target or producer cell type but varied widely between different IAV strains. These data indicate that IAV exists primarily as a swarm of complementation-dependent semi-infectious virions, and thus traditional, propagation-dependent assays of infectivity may drastically misrepresent the true infectious potential of a virus population.

Continue reading

It Rains Bullshit After Hurricanes

So far we have presented a lot of really cool papers, but today I want to talk about a paper that looks incredibly cool in a whole bunch of different ways in the abstract, introduction, and discussion but for whom much of that awesomeness falls apart under closer inspection of the results, methods, and context.  In it, the authors report their results having flown in NASA’s venerable old DC-8 across the US and down the west coast as well as through a couple of hurricanes with a filter designed to capture bacteria sized particles hanging out the side.  They then took the filter and analyzed it with fluorescent dyes and microscopes as well as genomically to see what was there.  In their paper they appear to arrive at five different major conclusions: that viable bacterial cells represented on average around 20% of the total particles in the 0.25- to 1-μm diameter range; that 60 to 100% of the 1.5 × 105 cells m−3 they saw were viable; that bacteria are at least two orders of magnitude more abundant than fungal cells in the troposphere; and that fecal coliforms represent a significant amount of the microbiota of hurricanes after landfall. Additionally, what has made the most splash though, is their speculation that because some of the taxa they determined were present by small subunit rRNA sequencing (See previously) had been shown to metabolize oxalic acid, a major chemical component of clouds, it was plausible that there was active bacterial metabolism happening in the clouds they analyzed.  Unfortunately, despite the journal it is published in and glowing praise from excellent blogs like Not Exactly Rocket Science, Climate Central, WiredMetafilter, and The Scientist, the speculation is pretty foolish and each of these conclusions is either inherently false, actively misleading, or very difficult to support with their data.

Here is the paper:

Microbiome of the upper troposphere: Species composition and prevalence, effects of tropical storms, and atmospheric implications

N DeLeon-Rodriguez, TL Lathem, LM Rodriguez-R, et al. Published 2013 in PNAS. doi: 10.1073/pnas.1212089110

The composition and prevalence of microorganisms in the middle-to-upper troposphere (8–15 km altitude) and their role in aerosol-cloud-precipitation interactions represent important, unresolved questions for biological and atmospheric science. In particular, airborne microorganisms above the oceans remain essentially uncharacterized, as most work to date is restricted to samples taken near the Earth’s surface. Here we report on the microbiome of low- and high-altitude air masses sampled onboard the National Aeronautics and Space Administration DC-8 platform during the 2010 Genesis and Rapid Intensification Processes campaign in the Caribbean Sea. The samples were collected in cloudy and cloud-free air masses before, during, and after two major tropical hurricanes, Earl and Karl. Quantitative PCR and microscopy revealed that viable bacterial cells represented on average around 20% of the total particles in the 0.25- to 1-μm diameter range and were at least an order of magnitude more abundant than fungal cells, suggesting that bacteria represent an important and underestimated fraction of micrometer-sized atmospheric aerosols. The samples from the two hurricanes were characterized by significantly different bacterial communities, revealing that hurricanes aerosolize a large amount of new cells. Nonetheless, 17 bacterial taxa, including taxa that are known to use C1–C4 carbon compounds present in the atmosphere, were found in all samples, indicating that these organisms possess traits that allow survival in the troposphere. The findings presented here suggest that the microbiome is a dynamic and underappreciated aspect of the upper troposphere with potentially important impacts on the hydrological cycle, clouds, and climate.

187071Credit:  http://www.gatech.edu/research/news/study-finds-substantial-microorganism-populations-upper-troposphere

Continue reading

An exciting and totally novel way to clinically address obesity.

Last year the M.D. Anderson Cancer Center started a Phase I clinical trial for a very interesting peptide based drug on the power of the counterintuitively awesome paper that I’m going to present today.  If it works in humans as well and as safely as it does in three other Old World primates it has the potential to be a game changer for the treatment of metabolic syndrome; the primary driver of obesity, Type II diabetes, and heart disease.

A Peptidomimetic Targeting White Fat Causes Weight Loss and Improved Insulin Resistance in Obese Monkeys

KF Barnhart, DR Christianson, PW Hanley, et al. Published 2011 in Sci Transl Med. DOI: 10.1126/scitranslmed.3002621 [REQUIRES FREE SUBSCRIPTION]

Obesity, defined as body mass index greater than 30, is a leading cause of morbidity and mortality and a financial burden worldwide. Despite significant efforts in the past decade, very few drugs have been successfully developed for the treatment of obese patients. Biological differences between rodents and primates are a major hurdle for translation of anti-obesity strategies either discovered or developed in rodents into effective human therapeutics. Here, we evaluate the ligand-directed peptidomimetic CKGGRAKDC-GG-D(KLAKLAK)2 (henceforth termed adipotide) in obese Old World monkeys. Treatment with adipotide induced targeted apoptosis within blood vessels of white adipose tissue and resulted in rapid weight loss and improved insulin resistance in obese monkeys. Magnetic resonance imaging and dual-energy x-ray absorptiometry confirmed a marked reduction in white adipose tissue. At experimentally determined optimal doses, monkeys from three different species displayed predictable and reversible changes in renal proximal tubule function. Together, these data in primates establish adipotide as a prototype in a new class of candidate drugs that may be useful for treating obesity in humans.

Rhesus macaques being adorableCredit: RedOrbit

Continue reading

A very neat new pathway in nerve cells

Vesicular Glycolysis Provides On-Board Energy for Fast Axonal Transport is an elegant paper that was published just recently in Cell. It quite effectively solves a really puzzling aspect of how nerves work that until now made absolutely no sense and has really cool implications for better understanding – and thus hopefully better treating – Huntington’s disease.  Here is a video where the authors present their paper:


Frédéric Saudou and colleagues explain why the glycolytic enzymes GAPDH and PGK are present on axonal vesicles: to provide a steady energy source that supplies the ATP necessary for fast axonal transport.

Here is the paper itself with its abstract:

Vesicular Glycolysis Provides On-Board Energy for Fast Axonal Transport

D Zala, MV Hinckelmann, Hua Yu, et al. Published 2013 in Cell. http://dx.doi.org/10.1016/j.cell.2012.12.029

Fast axonal transport (FAT) requires consistent energy over long distances to fuel the molecular motors that transport vesicles. We demonstrate that glycolysis provides ATP for the FAT of vesicles. Although inhibiting ATP production from mitochondria did not affect vesicles motility, pharmacological or genetic inhibition of the glycolytic enzyme GAPDH reduced transport in cultured neurons and in Drosophila larvae. GAPDH localizes on vesicles via a huntingtin-dependent mechanism and is transported on fast-moving vesicles within axons. Purified motile vesicles showed GAPDH enzymatic activity and produced ATP. Finally, we show that vesicular GAPDH is necessary and sufficient to provide on-board energy for fast vesicular transport. Although detaching GAPDH from vesicles reduced transport, targeting GAPDH to vesicles was sufficient to promote FAT in GAPDH deficient neurons. This specifically localized glycolytic machinery may supply constant energy, independent of mitochondria, for the processive movement of vesicles over long distances in axons.

Continue reading

Evolution in action, Nebraskan highways select for cliff sparrows with shorter wings

Sometimes research gives you answers to questions you didn’t even know you had when it is well designed. In this case researchers in Nebraska looking into the social behavior of cliff swallows, an especially communal type of bird with interesting implications for the selection of altruism, realized that they were seeing a lot less dead birds hit by cars and looked into why that might be happening with data they already had.

Cliff Swallows hanging out
Cliff Swallows hanging out under a highway in Texas
Credit: http://www.flickr.com/photos/tdavenport/3506561916/

Where has all the road kill gone?

CR Brown and NB Brown. Published 2013 in Curr. Biol. doi:10.1016/j.cub.2013.02.023

An estimated 80 million birds are killed by colliding with vehicles on U.S. roads each year [1], and millions more die annually in Europe [2] and elsewhere. Losses to vehicles are a serious problem for which various changes in roadway design and maintenance have been proposed [3]. Yet, given the magnitude of the mortality reported for some species [4], we might expect natural selection to favor individuals that either learn to avoid cars or that have other traits making them less likely to collide with vehicles. If so, the frequency of road kill should decline over time. No information is available for any species on whether the extent of road-associated mortality has changed [2]. During a 30-year study on social behavior and coloniality of cliff swallows (Petrochelidon pyrrhonota) in southwestern Nebraska, we found that the frequency of road-killed swallows declined sharply over the 30 years following the birds’ occupancy of roadside nesting sites and that birds killed on roads had longer wings than the population at large.

This all makes for a pretty neat demonstration of evolution by natural selection creating shifts in population features in response to new pressures, namely very fast very deadly cars.

Humans, non-human primates, and SNAKES!

A little more than a year ago, I walked through the rainforest following closely behind a large group of sooty mangabeys. A sharp call rang out, and within minutes, all hundred and twenty animals were gathered around a fallen tree, calling, staring, and poking and prodding something I couldn’t quite make out. “Wala! C’est un serpent!” my field assistant exclaimed – “Viper de Gabon!” And sure enough, after another few minutes of stress and irritation and noise and movement from the mangabeys, an immensely thick snake, maybe 6 feet long and exceptionally well camouflaged, slithered off in the opposite direction. Satisfied, the mangabeys moved on, but my spine was still shivery. That night, I dreamed that all the fallen logs in the forest were actually Gaboon vipers just waiting for me to step on them…

Many (if not most) primates respond with alarm calls to snakes. Many animals also engage in mobbing behavior (like the mangabeys), harassing the snake from a safe distance until they drive it away. It is likely that snakes played an active role in primate (and human) evolution as both predators and competitors of our ancestors, but unfortunately, the way that snakes consume their prey means that there is basically no fossil evidence of, say, an australopithecine that was eaten by a snake (unlike evidence of raptor predation on our ancestors). In this paper, the authors look at the relationship between snakes, non-human primates, and the best modern analogue for the lifestyle of human ancestors, modern hunting and gathering populations.

Bitis gabonica rhinoceros

Gaboon Viper
Wikimedia commons

Hunter-gatherers and other primates as prey, predators, and competitors of snakes.

Thomas N. Headland and Harry W. Greene. Proceedings of the National Academy of Sciences 108(52): E1470-E1474.

Relationships between primates and snakes are of widespread interest from anthropological, psychological, and evolutionary perspectives, but surprisingly, little is known about the dangers that serpents have posed to people with prehistoric lifestyles and nonhuman primates. Here, we report ethnographic observations of 120 Philippine Agta Negritos when they were still preliterate hunter–gatherers, among whom 26% of adult males had survived predation attempts by reticulated pythons. Six fatal attacks occurred between 1934 and 1973. Agta ate pythons as well as deer, wild pigs, and monkeys, which are also eaten by pythons, and therefore, the two species were reciprocally prey, predators, and potential competitors. Natural history data document snake predation on tree shrews and 26 species of nonhuman primates as well as many species of primates approaching, mobbing, killing, and sometimes eating snakes. These findings, interpreted within the context of snake and primate phylogenies, corroborate the hypothesis that complex ecological interactions have long characterized our shared evolutionary history.

Continue reading

Building Climate Change Predictions into Protected Area Management

Today I’d like to talk about a paper on a subject very close to my own scientific heart: Protected areas and climate change. I am a graduate assistant on a project that is looking at ways to improve a regional protected area network to increase resistance to climate change, and while I won’t be talking directly about my own project I’d like to present a meta-analysis of the state of research into that subject as of right now. This paper provides an interesting look into the kinds of questions and issues that conservation biologists are thinking about today, in a field where conservationists very often find themselves needing to account for multiple environmental threats simultaneously – climate change and habitat loss chief among them. Protected areas play what is in my opinion the most important role in conservation today (an opinion which I will argue at you in great detail over a beer if you ever care to buy me one) and strengthening and preserving them is critical to the preservation of biodiversity on this planet.

Current models broadly neglect specific needs of biodiversity conservation in protected areas under climate change

M. Sieck, P.L. Ibisch, K.A. Moloney, & F. Jeltsch. BMC Ecology, 2011. doi:10.1186/1472-6785-11-12

The visualization below provides a nice overview of the problem, but for those like myself who are a bit more textually inclined, I’ll give a a brief summary. Climate change is altering ecosystems around the globe, raising temperatures and warming habitats. As habitats warm, many species are predicted to shift their ranges a bit closer to the poles or up to higher altitudes, in order to remain within their preferred temperature range as much as possible. Obviously some species are going to have an easier time of this than others, and some habitats are going to be more conducive to shifting than others. Of particular concern are species which are dependent upon parks and other protected areas, since if their protected zones become unsuitable for them they may find themselves forced out into unprotected areas where they will face greater threat from human activity. This is a problem of which conservation biologists have been aware for some time, but it is a complicated enough phenomenon that we have rarely been able to make satisfactory predictions about where the greatest vulnerabilities lie and what the best steps would be to augment the global network of protected areas in order to mitigate those vulnerabilities. As I said, the visualization below gives a nice overview.

Today’s paper is a meta-analysis published in 2011, which looked at a broad swath of scientific literature focused on the subject of protected areas and climate change, all published between 1998 and 2010. It attempts to describe the historic research trends in that field of inquiry, to identify what some of the biggest gaps are, and to make recommendations about how future researchers (such as myself and the scientists who I work with) might address some of those historic shortcomings in their own research.

In this review, we examine and evaluate trends and gaps in current modeling approaches of climate change impacts on protected areas. More specifically we ask whether current modeling approaches are appropriate and sufficient to aid us in protecting species diversity within protected areas under changing climatic conditions. Focusing on terrestrial protected areas, we aim to provide a useful overview and generate guidelines for future research in order to establish adaptive and ‘climate-proof’ conservation strategies for protected areas.

We review the existing literature on the topic over the last twelve years (1998 – June 2010). The focus lies on the evaluation of (i) current modeling approaches and their usage in the fields of conservation biology and ecological forecasting of protected areas, (ii) the species or species groups of main interest, (iii) implementation of additional threats and key processes in the models, e.g., land-use, habitat fragmentation, invasion and dispersal, and (iv) the testing and implementation of specific management actions.

Let’s see what they found, shall we? Continue reading